MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000332831
MT speed 0 s - this script 2.981 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
OR4F16	polymorphism	2.95985458365067e-13	simple_aae		affected		V219I	single base exchange			show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999704 (explain)

Summary

amino acid sequence changed
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:621380C>TN/A show variant in all transcripts IGV

HGNC symbol

OR4F16

Ensembl transcript ID

ENST00000332831

Genbank transcript ID

NM_001005277

UniProt peptide

Q6IEY1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.655G>A
cDNA.674G>A
g.674G>A

AA changes

V219I Score: 29 explain score(s)

position(s) of altered AA
if AA alteration in CDS

219

frameshift

known variant

Variant was neither found in ExAC nor 1000G.
Search ExAC.

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.872	0.005
	-0.775	0.006
(flanking)	0.003	0.106

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	671	wt: 0.2031 / mu: 0.2397 (marginal change - not scored)	wt: TCTTCATACTTCTAATCTCCTACGTCTTCATCCTGTTTACT mu: TCTTCATACTTCTAATCTCCTACATCTTCATCCTGTTTACT	tcct\|ACGT
Acc marginally increased	680	wt: 0.4434 / mu: 0.4747 (marginal change - not scored)	wt: TTCTAATCTCCTACGTCTTCATCCTGTTTACTGTTTGGAAA mu: TTCTAATCTCCTACATCTTCATCCTGTTTACTGTTTGGAAA	ttca\|TCCT
Acc increased	665	wt: 0.39 / mu: 0.47	wt: GTACTTTCTTCATACTTCTAATCTCCTACGTCTTCATCCTG mu: GTACTTTCTTCATACTTCTAATCTCCTACATCTTCATCCTG	ctaa\|TCTC
Acc increased	677	wt: 0.34 / mu: 0.61	wt: TACTTCTAATCTCCTACGTCTTCATCCTGTTTACTGTTTGG mu: TACTTCTAATCTCCTACATCTTCATCCTGTTTACTGTTTGG	gtct\|TCAT

distance from splice site

322

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

219

mutated

all conserved

219

Ptroglodytes

all identical

ENSPTRG00000031387

219

Mmulatta

all conserved

ENSMMUG00000016419

219

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
196	219	TRANSMEM	Helical; Name=5; (Potential).	lost
220	235	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
236	258	TRANSMEM	Helical; Name=6; (Potential).	might get lost (downstream of altered splice site)
259	269	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
270	289	TRANSMEM	Helical; Name=7; (Potential).	might get lost (downstream of altered splice site)
290	312	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

939 / 939

position (AA) of stopcodon in wt / mu AA sequence

313 / 313

position of stopcodon in wt / mu cDNA

958 / 958

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

20 / 20

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

939

coding sequence (CDS) position

655

cDNA position
(for ins/del: last normal base / first normal base)

674

gDNA position
(for ins/del: last normal base / first normal base)

674

chromosomal position
(for ins/del: last normal base / first normal base)

621380

original gDNA sequence snippet

TCATACTTCTAATCTCCTACGTCTTCATCCTGTTTACTGTT

altered gDNA sequence snippet

TCATACTTCTAATCTCCTACATCTTCATCCTGTTTACTGTT

original cDNA sequence snippet

TCATACTTCTAATCTCCTACGTCTTCATCCTGTTTACTGTT

altered cDNA sequence snippet

TCATACTTCTAATCTCCTACATCTTCATCCTGTTTACTGTT

wildtype AA sequence

MDGENHSVVS EFLFLGLTHS WEIQLLLLVF SSVLYVASIT GNILIVFSVT TDPHLHSPMY
FLLASLSFID LGACSVTSPK MIYDLFRKRK VISFGGCIAQ IFFIHVVGGV EMVLLIAMAF
DRYVALCKPL HYLTIMSPRM CLSFLAVAWT LGVSHSLFQL AFLVNLAFCG PNVLDSFYCD
LPRLLRLACT DTYRLQFMVT VNSGFICVGT FFILLISYVF ILFTVWKHSS GGSSKALSTL
SAHSTVVLLF FGPPMFVYTR PHPNSQMDKF LAIFDAVLTP FLNPVVYTFR NKEMKAAIKR
VCKQLVIYKR IS*

mutated AA sequence

MDGENHSVVS EFLFLGLTHS WEIQLLLLVF SSVLYVASIT GNILIVFSVT TDPHLHSPMY
FLLASLSFID LGACSVTSPK MIYDLFRKRK VISFGGCIAQ IFFIHVVGGV EMVLLIAMAF
DRYVALCKPL HYLTIMSPRM CLSFLAVAWT LGVSHSLFQL AFLVNLAFCG PNVLDSFYCD
LPRLLRLACT DTYRLQFMVT VNSGFICVGT FFILLISYIF ILFTVWKHSS GGSSKALSTL
SAHSTVVLLF FGPPMFVYTR PHPNSQMDKF LAIFDAVLTP FLNPVVYTFR NKEMKAAIKR
VCKQLVIYKR IS*

speed

0.98 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems